I also use that cheap PCB from rapid, but tend to need the bigger sheets.

Have you considered toner transfer, where you print the mirrored artwork off using a laser printer onto the correct type of paper, place it over the bare board, iron it on then etch as normal? I've used it quite a lot and you can do very accurate boards with a bit care. The best paper is the type that sticky labels peel off as the toner doesn't stick very well to it. The finest I did was an 80-pin TQFP as a test. PCB was fine but I couldn't solder it!

Anyway, clearly milling PCBs is superior. Whilst selecting the track outlines and offsetting them to create the toolpaths works, if you're trying to make fine board it can be difficult to ensure pieces don't overlap. So instead I convert the tracks to the minimum required lines to isolate each connection.

From this:
(drawn with funny pads/track widths to make conversion easier)
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To this:

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Unless you're doing fancy RF stuff the odd shape tracks shouldn't be a problem. It's also less cutting, so clearly tools last longer and it doesn't take as long to cut. The latter isn't really an advantage unless you're making several of the same as it takes a while to redraw it.

As long as you don't skimp on the stepper motor and drivers there's no reason to expect long term problems with missed steps. This is particularly important since you seem to have chosen a relatively heavy machine bed with dovetail slides, not rolling balls, so the total force required by the stepper motors (F=uC+ma) will be high compared to a moving gantry router if you want to get decent acceleration and speed, which you do for PCBs since they have a lot of short moves and changes of direction.